Add a simple unit test which queries laminlabs/lamindata (#27)

* Add a simple unit test which queries laminlabs/lamindata

* update changelog

* Add `skip_if_offline`

* use text figures

* add newline

.github/workflows/R-CMD-check.yaml

@@ -46,7 +46,7 @@ jobs:
 
       - name: Install lamindb
         run: |
-          pip install lamindb[bionty]
+          pip install lamindb[bionty,wetlab]
 
       - name: Log in to Lamin
         run: |

.github/workflows/pkgdown.yaml

@@ -44,7 +44,7 @@ jobs:
 
       - name: Install lamindb
         run: |
-          pip install lamindb[bionty]
+          pip install lamindb[bionty,wetlab]
 
       - name: Log in to Lamin
         run: |

CHANGELOG.md

@@ -35,6 +35,8 @@
 
 * Define a current user and current instance with lamin-cli prior to testing and generating documentation in the CI (PR #23).
 
+* Add a simple unit test which queries laminlabs/lamindata (PR #27).
+
 ## BUG FIXES
 
 * Fixed the parsing of the env files in `~/.lamin` due to changes in the lamindb-setup Python package (PR #12).

DESCRIPTION

@@ -26,5 +26,8 @@ Imports:
 Suggests:
     anndata,
     quarto,
-    s3 (>= 1.1.0)
+    s3 (>= 1.1.0),
+    testthat (>= 3.0.0),
+    withr
 VignetteBuilder: quarto
+Config/testthat/edition: 3

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(laminr)
+
+test_check("laminr")

tests/testthat/helper-setup_lamindata_instance.R

@@ -0,0 +1,42 @@
+local_setup_lamindata_instance <- function(env = parent.frame()) {
+  root_dir <- withr::local_file(tempfile(), .local_envir = env)
+  withr::local_envvar(c(LAMIN_SETTINGS_DIR = root_dir), .local_envir = env)
+
+  # create a temporary directory for the settings
+  lamin_dir <- file.path(root_dir, ".lamin")
+  dir.create(lamin_dir, recursive = TRUE, showWarnings = FALSE)
+
+  # generate user settings
+  user_settings <- list(
+    email = "null",
+    password = "null",
+    access_token = "null",
+    api_key = "null",
+    uid = "00000000",
+    uuid = "null",
+    handle = "anonymous",
+    name = "null"
+  )
+  user_lines <- paste0("lamin_user_", names(user_settings), "=", unlist(user_settings))
+  writeLines(user_lines, file.path(lamin_dir, "current_user.env"))
+
+  # generate instance settings
+  instance_settings <- list(
+    owner = "laminlabs",
+    name = "lamindata",
+    api_url = "https://us-east-1.api.lamin.ai",
+    storage_root = "s3://lamindata",
+    storage_region = "us-east-1",
+    db = "null",
+    schema_str = "bionty,wetlab",
+    schema_id = "097186c3e91c01ced47aa3e01a3c1515",
+    id = "037ba1e08d804f91a90275a47735076a",
+    git_repo = "null",
+    keep_artifacts_local = "False"
+  )
+  instance_lines <- paste0("lamindb_instance_", names(instance_settings), "=", unlist(instance_settings))
+  writeLines(instance_lines, file.path(lamin_dir, "current_instance.env"))
+  writeLines(instance_lines, file.path(lamin_dir, "instance--laminlabs--lamindata.env"))
+
+  root_dir
+}

tests/testthat/test-connect_lamindata.R

@@ -0,0 +1,21 @@
+skip_if_offline()
+
+test_that("Connecting to lamindata works", {
+  local_setup_lamindata_instance()
+
+  # try to connect to lamindata
+  db <- connect("laminlabs/lamindata")
+
+  # check whether schema was parsed and classes were created
+  expect_equal(db$Artifact$name, "artifact")
+
+  # try to fetch a record
+  artifact <- db$Artifact$get("mePviem4DGM4SFzvLXf3")
+
+  expect_equal(artifact$uid, "mePviem4DGM4SFzvLXf3")
+  expect_equal(artifact$suffix, ".csv")
+
+  # try to fetch linked records
+  created_by <- artifact$created_by
+  expect_equal(created_by$handle, "sunnyosun")
+})